Genome-Wide Discovery of Drug-Dependent Human Liver Regulatory Elements

Robin P. Smith, Walter L. Eckalbar, Kari M. Morrissey, Marcelo R. Luizon, Thomas J. Hoffmann, Xuefeng Sun, Stacy L. Jones, Shelley Force Aldred, Anuradha Ramamoorthy, Zeruesenay Desta, Yunlong Liu, Todd Skaar, Nathan D. Trinklein, Kathleen M. Giacomini, Nadav Ahituv

Research output: Contribution to journalArticle

15 Citations (Scopus)

Abstract

Inter-individual variation in gene regulatory elements is hypothesized to play a causative role in adverse drug reactions and reduced drug activity. However, relatively little is known about the location and function of drug-dependent elements. To uncover drug-associated elements in a genome-wide manner, we performed RNA-seq and ChIP-seq using antibodies against the pregnane X receptor (PXR) and three active regulatory marks (p300, H3K4me1, H3K27ac) on primary human hepatocytes treated with rifampin or vehicle control. Rifampin and PXR were chosen since they are part of the CYP3A4 pathway, which is known to account for the metabolism of more than 50% of all prescribed drugs. We selected 227 proximal promoters for genes with rifampin-dependent expression or nearby PXR/p300 occupancy sites and assayed their ability to induce luciferase in rifampin-treated HepG2 cells, finding only 10 (4.4%) that exhibited drug-dependent activity. As this result suggested a role for distal enhancer modules, we searched more broadly to identify 1,297 genomic regions bearing a conditional PXR occupancy as well as all three active regulatory marks. These regions are enriched near genes that function in the metabolism of xenobiotics, specifically members of the cytochrome P450 family. We performed enhancer assays in rifampin-treated HepG2 cells for 42 of these sequences as well as 7 sequences that overlap linkage-disequilibrium blocks defined by lead SNPs from pharmacogenomic GWAS studies, revealing 15/42 and 4/7 to be functional enhancers, respectively. A common African haplotype in one of these enhancers in the GSTA locus was found to exhibit potential rifampin hypersensitivity. Combined, our results further suggest that enhancers are the predominant targets of rifampin-induced PXR activation, provide a genome-wide catalog of PXR targets and serve as a model for the identification of drug-responsive regulatory elements.

Original languageEnglish
JournalPLoS Genetics
Volume10
Issue number10
DOIs
StatePublished - Oct 1 2014

Fingerprint

rifampicin
Drug Discovery
Rifampin
drug
genome
Genome
drugs
liver
Liver
receptors
Pharmaceutical Preparations
Hep G2 Cells
gene
metabolism
pharmacogenomics
Cytochrome P-450 CYP3A
Genome-Wide Association Study
Linkage Disequilibrium
individual variation
Xenobiotics

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology
  • Ecology, Evolution, Behavior and Systematics
  • Cancer Research
  • Genetics(clinical)

Cite this

Smith, R. P., Eckalbar, W. L., Morrissey, K. M., Luizon, M. R., Hoffmann, T. J., Sun, X., ... Ahituv, N. (2014). Genome-Wide Discovery of Drug-Dependent Human Liver Regulatory Elements. PLoS Genetics, 10(10). https://doi.org/10.1371/journal.pgen.1004648

Genome-Wide Discovery of Drug-Dependent Human Liver Regulatory Elements. / Smith, Robin P.; Eckalbar, Walter L.; Morrissey, Kari M.; Luizon, Marcelo R.; Hoffmann, Thomas J.; Sun, Xuefeng; Jones, Stacy L.; Force Aldred, Shelley; Ramamoorthy, Anuradha; Desta, Zeruesenay; Liu, Yunlong; Skaar, Todd; Trinklein, Nathan D.; Giacomini, Kathleen M.; Ahituv, Nadav.

In: PLoS Genetics, Vol. 10, No. 10, 01.10.2014.

Research output: Contribution to journalArticle

Smith, RP, Eckalbar, WL, Morrissey, KM, Luizon, MR, Hoffmann, TJ, Sun, X, Jones, SL, Force Aldred, S, Ramamoorthy, A, Desta, Z, Liu, Y, Skaar, T, Trinklein, ND, Giacomini, KM & Ahituv, N 2014, 'Genome-Wide Discovery of Drug-Dependent Human Liver Regulatory Elements', PLoS Genetics, vol. 10, no. 10. https://doi.org/10.1371/journal.pgen.1004648
Smith RP, Eckalbar WL, Morrissey KM, Luizon MR, Hoffmann TJ, Sun X et al. Genome-Wide Discovery of Drug-Dependent Human Liver Regulatory Elements. PLoS Genetics. 2014 Oct 1;10(10). https://doi.org/10.1371/journal.pgen.1004648
Smith, Robin P. ; Eckalbar, Walter L. ; Morrissey, Kari M. ; Luizon, Marcelo R. ; Hoffmann, Thomas J. ; Sun, Xuefeng ; Jones, Stacy L. ; Force Aldred, Shelley ; Ramamoorthy, Anuradha ; Desta, Zeruesenay ; Liu, Yunlong ; Skaar, Todd ; Trinklein, Nathan D. ; Giacomini, Kathleen M. ; Ahituv, Nadav. / Genome-Wide Discovery of Drug-Dependent Human Liver Regulatory Elements. In: PLoS Genetics. 2014 ; Vol. 10, No. 10.
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